{ "type": "genome", "identifier": "GCF_019977755.1", "organism": "Vibrio penaeicida", "title": "Vibrio penaeicida", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Laboratory of Genome Science Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology", "publication": [ {} ], "properties": { "assembly_accession": "GCF_019977755.1", "bioproject": "PRJNA224116", "biosample": "SAMD00318911", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "104609", "species_taxid": "104609", "organism_name": "Vibrio penaeicida", "infraspecific_name": "strain=IFO 15640T", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/09/09", "asm_name": "ASM1997775v1", "asm_submitter": "Laboratory of Genome Science Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology", "gbrs_paired_asm": "GCA_019977755.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/019/977/755/GCF_019977755.1_ASM1997775v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6782963", "genome_size_ungapped": "6782963", "gc_percent": "44.000000", "replicon_count": "3", "scaffold_count": "3", "contig_count": "3", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_019977755.1-RS_2024_11_06", "annotation_date": "2024-11-06", "total_gene_count": "6034", "protein_coding_gene_count": "5812", "non_coding_gene_count": "144", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-09-09", "dateModified": "2021-09-09", "datePublished": "2021-09-09", "_annotation": { "sample_count": 1, "sample_organism": [ "Vibrio penaeicida" ], "sample_taxid": [ "104609" ], "sample_host_organism": [ "Penaeus japonicus" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "1.928 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "6782963", "Number of Sequences": "3", "Longest Sequences (bp)": "4134604", "N50 (bp)": "4134604", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "43.9", "Number of CDSs": "5942", "Average Protein Length": "329.0", "Coding Ratio (%)": "86.5", "Number of rRNAs": "31", "Number of tRNAs": "109", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Vibrio penaeicida", "strain": "strain=IFO 15640", "accession": "GCA_019977755.1", "taxid": 104609, "species_taxid": 104609, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2258, "total_fragments": 2260, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Vibrio penaeicida", "strain": "strain=CAIM 285", "accession": "GCA_003970425.1", "taxid": 104609, "species_taxid": 104609, "relation_to_type": "type", "validated": true, "ani": 99.8236, "matched_fragments": 1878, "total_fragments": 2260, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Vibrio nigripulchritudo", "strain": "strain=ATCC 27043", "accession": "GCA_000222685.2", "taxid": 28173, "species_taxid": 28173, "relation_to_type": "type", "validated": true, "ani": 81.8091, "matched_fragments": 964, "total_fragments": 2260, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio tubiashii", "strain": "strain=ATCC 19109", "accession": "GCA_000772105.1", "taxid": 29498, "species_taxid": 29498, "relation_to_type": "suspected-type", "validated": true, "ani": 80.2861, "matched_fragments": 318, "total_fragments": 2260, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio pelagius", "strain": "strain=ATCC 25916", "accession": "GCA_024347575.1", "taxid": 28169, "species_taxid": 28169, "relation_to_type": "type", "validated": true, "ani": 80.2498, "matched_fragments": 293, "total_fragments": 2260, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio pomeroyi", "strain": "strain=LMG 20537", "accession": "GCA_024347595.1", "taxid": 198832, "species_taxid": 198832, "relation_to_type": "type", "validated": true, "ani": 80.22, "matched_fragments": 296, "total_fragments": 2260, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio parahaemolyticus", "strain": "strain=NCTC10903", "accession": "GCA_900460535.1", "taxid": 670, "species_taxid": 670, "relation_to_type": "type", "validated": true, "ani": 80.1905, "matched_fragments": 303, "total_fragments": 2260, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio chagasii", "strain": "strain=LMG 21353", "accession": "GCA_024347355.1", "taxid": 170679, "species_taxid": 170679, "relation_to_type": "suspected-type", "validated": true, "ani": 80.1578, "matched_fragments": 313, "total_fragments": 2260, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio crassostreae", "strain": "strain=LMG 22240", "accession": "GCA_024347415.1", "taxid": 246167, "species_taxid": 246167, "relation_to_type": "type", "validated": true, "ani": 80.1198, "matched_fragments": 324, "total_fragments": 2260, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio toranzoniae", "strain": "strain=CECT 7225", "accession": "GCA_024347655.1", "taxid": 1194427, "species_taxid": 1194427, "relation_to_type": "type", "validated": true, "ani": 79.9445, "matched_fragments": 302, "total_fragments": 2260, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio europaeus", "strain": "strain=PP-638", "accession": "GCA_001695575.1", "taxid": 300876, "species_taxid": 300876, "relation_to_type": "type", "validated": true, "ani": 79.8575, "matched_fragments": 324, "total_fragments": 2260, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio cortegadensis", "strain": "strain=CECT 7227", "accession": "GCA_024347395.1", "taxid": 1328770, "species_taxid": 1328770, "relation_to_type": "type", "validated": true, "ani": 79.78, "matched_fragments": 290, "total_fragments": 2260, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio tubiashii", "strain": "strain=ATCC 19109", "accession": "GCA_000222665.2", "taxid": 29498, "species_taxid": 29498, "relation_to_type": "suspected-type", "validated": true, "ani": 79.6424, "matched_fragments": 303, "total_fragments": 2260, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio coralliilyticus", "strain": "strain=ATCC BAA-450", "accession": "GCA_000176135.1", "taxid": 190893, "species_taxid": 190893, "relation_to_type": "type", "validated": true, "ani": 79.6274, "matched_fragments": 284, "total_fragments": 2260, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio aquaticus", "strain": "strain=BEI207", "accession": "GCA_003970385.1", "taxid": 2496559, "species_taxid": 2496559, "relation_to_type": "type", "validated": true, "ani": 79.4085, "matched_fragments": 303, "total_fragments": 2260, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio parahaemolyticus", "strain": "strain=ATCC 17802", "accession": "GCA_001011015.1", "taxid": 670, "species_taxid": 670, "relation_to_type": "type", "validated": true, "ani": 79.3688, "matched_fragments": 285, "total_fragments": 2260, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio bivalvicida", "strain": "strain=605", "accession": "GCA_001399455.2", "taxid": 1276888, "species_taxid": 1276888, "relation_to_type": "type", "validated": true, "ani": 79.174, "matched_fragments": 283, "total_fragments": 2260, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio nereis", "strain": "strain=NBRC 15637", "accession": "GCA_001591105.1", "taxid": 693, "species_taxid": 693, "relation_to_type": "type", "validated": true, "ani": 79.0991, "matched_fragments": 272, "total_fragments": 2260, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio scophthalmi", "strain": "strain=LMG 19158", "accession": "GCA_000222585.2", "taxid": 45658, "species_taxid": 45658, "relation_to_type": "type", "validated": true, "ani": 78.9866, "matched_fragments": 248, "total_fragments": 2260, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio sonorensis", "strain": "strain=CAIM 1076", "accession": "GCA_001854765.1", "taxid": 1004316, "species_taxid": 1004316, "relation_to_type": "type", "validated": true, "ani": 78.8406, "matched_fragments": 258, "total_fragments": 2260, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vibrio aestuarianus subsp. cardii", "strain": "strain=12/122 3T3", "accession": "GCA_011090275.1", "taxid": 2807650, "species_taxid": 28171, "relation_to_type": "type", "validated": true, "ani": 78.7952, "matched_fragments": 267, "total_fragments": 2260, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003970425.1", "gtdb_species": "s__Vibrio penaeicida", "ani": 99.8213, "matched_fragments": 1879, "total_fragments": 2260, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.14", "min_intra_species_ani": "96.14", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.85", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_002933855.1", "gtdb_species": "s__Vibrio penaeicida_A", "ani": 92.6081, "matched_fragments": 1816, "total_fragments": 2260, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_014694455.1", "gtdb_species": "s__Vibrio sp014694455", "ani": 85.4618, "matched_fragments": 1422, "total_fragments": 2260, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_000222685.1", "gtdb_species": "s__Vibrio nigripulchritudo", "ani": 81.8314, "matched_fragments": 958, "total_fragments": 2260, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.90", "min_intra_species_ani": "96.77", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.87", "num_clustered_genomes": 18, "status": "-" }, { "accession": "GCF_000772105.1", "gtdb_species": "s__Vibrio tubiashii", "ani": 80.3342, "matched_fragments": 315, "total_fragments": 2260, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.61", "min_intra_species_ani": "95.85", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.87", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_900233005.1", "gtdb_species": "s__Vibrio tapetis", "ani": 79.4911, "matched_fragments": 362, "total_fragments": 2260, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_000775715.1", "gtdb_species": "s__Vibrio tubiashii_A", "ani": 79.4575, "matched_fragments": 274, "total_fragments": 2260, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_003970385.1", "gtdb_species": "s__Vibrio aquaticus", "ani": 79.4436, "matched_fragments": 302, "total_fragments": 2260, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_000808535.1", "gtdb_species": "s__Vibrio sinaloensis", "ani": 79.4234, "matched_fragments": 279, "total_fragments": 2260, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.52", "min_intra_species_ani": "97.23", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.89", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_009938165.1", "gtdb_species": "s__Vibrio taketomensis", "ani": 79.3116, "matched_fragments": 268, "total_fragments": 2260, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.31", "min_intra_species_ani": "98.31", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_009811315.1", "gtdb_species": "s__Vibrio atypicus", "ani": 79.1114, "matched_fragments": 316, "total_fragments": 2260, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.15", "min_intra_species_ani": "97.15", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000189255.1", "gtdb_species": "s__Vibrio brasiliensis", "ani": 79.0838, "matched_fragments": 269, "total_fragments": 2260, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_000222585.1", "gtdb_species": "s__Vibrio scophthalmi", "ani": 79.0042, "matched_fragments": 247, "total_fragments": 2260, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.31", "min_intra_species_ani": "96.70", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.84", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCA_018223135.1", "gtdb_species": "s__Vibrio sp018223135", "ani": 78.8758, "matched_fragments": 264, "total_fragments": 2260, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.302, "cell_length": 0.176, "doubling_h": -0.527, "growth_tmp": 26.0, "optimum_tmp": 30.0, "optimum_ph": 7.4, "genome_size": 6412606.0, "gc_content": 43.857, "coding_genes": 4624.827, "rRNA16S_genes": 10.063, "tRNA_genes": 116.411, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": 0.923, "facultative_respiration": 1.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.0, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 0.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 1.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Vibrio", "penaeicida" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }